GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Herbaspirillum seropedicae SmR1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__HerbieS:HSERO_RS05420
          Length = 426

 Score =  196 bits (498), Expect = 1e-54
 Identities = 134/379 (35%), Positives = 207/379 (54%), Gaps = 30/379 (7%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKTL 133
           L D +G+ FID   G  + N GHR+P ++ A++ Q+ K   H+   + P  +   LA+ +
Sbjct: 38  LWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFT-HTAYQIVPYASYVELAERI 96

Query: 134 AALTPGKL-KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192
             LTPG   K + F ++G E+VE A+K+A+A+    G    IA +G FHG+++  ++ T 
Sbjct: 97  NRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPG---VIAFAGGFHGRTMMGMALTG 153

Query: 193 K-STFRKPFMPLLPGFRHVPFGN----------IEAMRTALNECKKTGDDVAAVILEPIQ 241
           K + ++  F P      H P+ +          +EA++  L +       VAA+ILEP+Q
Sbjct: 154 KVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVK-GLFKSDIEAKRVAAIILEPVQ 212

Query: 242 GEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKA 301
           GEGG    P  ++  +R LCDE G L+I DEVQ+G GRTGK+FA EH +V PD++ +AK+
Sbjct: 213 GEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKS 272

Query: 302 LGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQ 361
           L GG MP+ A     E+       P     T+ GNPLA A+ALA ++V+ E+ L  + ++
Sbjct: 273 LAGG-MPLSAVNGRAEIMDA--PAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQR 329

Query: 362 KGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFA--SEMFRQRVLVAGTL 419
            GD L +  ++L    P  + E RG G ++A+EF D   G   A  ++  +Q  L  G L
Sbjct: 330 LGDKLQEHLKELRSSVPQ-IAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLL 388

Query: 420 -----NNAKTIRIEPPLTL 433
                +    IR   PLT+
Sbjct: 389 LLTCGSYGNVIRFLFPLTI 407


Lambda     K      H
   0.320    0.135    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 443
Number of extensions: 24
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 459
Length of database: 426
Length adjustment: 32
Effective length of query: 427
Effective length of database: 394
Effective search space:   168238
Effective search space used:   168238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory